HI Stephen,

not quite raw image space, but mostly. Definitely not tal coords. We resample into a 256^3 volume aligned with the native scanner coords.

cheers,
Bruce

On Wed, 30 Jul 2008, Stephen Rose wrote:

Hi

I am a new freesurfer user so I apologize in advance for the basic
questions.

If I already have my MPRAGE images in mgz format (i.e I don't need to
convert the raw dicom data with mri_convert), what changes to the
command line (below) do I need so that the all the correct data
directories are initially set up (and not call mri_convert)?

recon-all -i  <path-to-structural> -s <subjid>

When viewing the results of autorecon1 and 2 are all the surfaces and
segmentation results shown in raw image space and not Talairach space?

Thanks for your help
Stephen



A/Prof. Stephen Rose
Principal Research Fellow
Centre for Magnetic Resonance
Centre for Clinical Research
University of Queensland
Brisbane, QLD, 4072 Australia
Telephone: +61 7 33466101
Mobile: 0412023958
Fax: +61 7 33653833

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